Proteopedia:News

This page is for external news reports etc. about Proteopedia. For new pages and capabilities within Proteopedia, please see Proteopedia:What's New.

Add New Items at the Top of Each Section and Date Them, Please!
News on this page is ordered newest first, oldest last, under each subheading. Please include the month and year at the end of each entry that you add below. Subheadings below Statistics are in alphabetical order.

Statistics
Today, Proteopedia has registered users. For more information, please see Proteopedia:About. For the number of pages, page views, edits, etc. please see Special:Statistics. The number of times any page has been viewed is displayed at the bottom of the page.

Publication

 * Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121

Adoptions by Structural Bioinformatics Resources
Some bioinformatics databases and resources have adopted Proteopedia. This means that they have chosen to offer links to Proteopedia for the benefit of their users.


 * ExPASy Proteomics Server (EXpert Protein Analysis SYstem) of the Swiss Institute of Bioinformatics offers links to Proteopedia on its 3D structure pages, e.g. PDB code: 1A5H. October, 2008.


 * TOPSAN, The Open Protein Structure Annotation Network, a wiki designed to collect, share and distribute information about protein three-dimensional structures. October, 2008.


 * Protein Crystallography Universe, a website provided by Rigaku Life Sciences Group, links Proteopedia under Structure Analysis and Reference Shelf. October, 2008.


 * CATH, a hierarchical classification of protein domain structures [Class (C), Architecture (A), Topology (T) and Homologous superfamily (H)], provides links on its PDB pages to Proteopedia. September, 2008.


 * GeneCards, a searchable, integrated database providing concise information on all known and predicted human genes, links relevant proteins to Proteopedia. September, 2008.


 * Jmol Tutorial-Authoring Template (JTAT) automatically provides a link to Proteopedia for each PDB file illustrated in its tutorials. August, 2008. See, for example, the bottom right (Explore further ... under How To ...) in the JTAT Demo Tutorial.


 * Molecule of the Month by David S. Goodsell provides links to Proteopedia in some recent articles. An example is linked at the end of the second page of the article on Selenocysteine Synthase. August, 2008. Here is the complete list.


 * OCA Database and Browser for 3D macromolecular structure has a link from each PDB entry to Proteopedia. August, 2008.


 * PDBsum has a link to Proteopedia on every PDB entry page. August, 2008.


 * PDBWiki has a link to Proteopedia on every PDB entry page. August, 2008.


 * RCSB Protein Data Bank (see Proteopedia's page on the Protein Data Bank), has a link from each PDB entry to Proteopedia, but it can be a bit hard to find. To find it: At the Structure Summary tab/page for a given PDB code, in the menu at left, click on External LInks. On that page, you'll find a link to Proteopedia under Structure Summary. If you think it would be useful to have a more prominent link to Proteopedia at RCSB-PDB, please email info@rcsb.org . In May, 2008, an international group of several structural bioinformaticians and crystallographers requested that a link to Proteopedia replace the present Jmol link under Display Options at the upper right of the main Structure Summary page for each entry, but that request was denied. Eric Martz 03:19, 7 August 2008 (IDT)


 * Pfam, a large database of protein families, each represented by multiple sequence alignments and hidden Markov models, will offer links to Proteopedia beginning with Pfam release 23. August, 2008.


 * PSI Structural Genomics Knowledge Base has a link to Proteopedia, on its Annotations tab, for every PDB entry. August, 2008.

Adoptions in University Classes
See also Student Projects, Teaching Scenes, Tutorials, and Educators' Pages, and Teaching Strategies Using Proteopedia.


 * Advanced Molecular Biology (Biochem 642, for graduate students) taught by Drs. Robert Zimmermann and Alice Cheung at the University of Massachusetts, Amherst. A two-session, hands-on workshop introducing First Glance in Jmol and Proteopedia's Scene authoring tools was taught by User:Wayne Decatur, who prepared Biochem642 Molecular Visualization Sessions and Teaching Proteopedia. Students were assigned problem sets that required authoring accompanying scenes in sandbox pages. November, 2009.


 * Biomolecular Structure (Chem 791a, for graduate students) taught by crystallographer Jeanne Hardy at the University of Massachusetts, Amherst. A computer lab workshop introducing the Scene authoring tools was taught by User:Wayne Decatur, who prepared Chem791A Work Session and Teaching Proteopedia. November, 2008.

Press

 * PDB Education Corner, Winter 2011
 * GENnews Best Of The Web: Proteopedia, May, 2010
 * The Scientist: "Structure Made Simple". March, 2010
 * Seed Magazine: "Scientific Truth in the Age of Wikipedia". February, 2009
 * Proteopedia in Faculty of 1000. October, 2008
 * Nature Reviews Molecular Cell Biology - October, 2008 Research highlights
 * Nature Cell Biology - October, 2008, Proteopedia mentioned in Editorial
 * GenomeBiology.com Press Release August, 2008

Blogs

 * edfed Proteopedia collects and disseminates information about molecules, February 8th, 2010
 * Molecular Modeling Basics October, 2009. A blog related to the book of the same name.
 * BeckerInfo.net Open Source Visualization December, 2008
 * car54.wordpress.com August, 2008
 * Wonder: Sci-Tech Department August 2008
 * The Scientist -- Richard Grant's blog on Nature Network March 2008
 * Peter Murray Rust's blog March, 2008

Press Release Re-Posts

 * mechanical engineering November, 2008
 * Science Daily August, 2008
 * The Wired Campus August, 2008
 * e! Science News August, 2008
 * Medical Health Articles August, 2008
 * YAHOO! News, India August, 2008
 * Proteopedia – pierwsza encyklopedia z trójwymiarową zawartością August, 2008
 * WEBINDIA123 August, 2008
 * pda.physorg.com August, 2008
 * Europe Sun August, 2008
 * AECC August, 2008
 * AlphaGalileo August, 2008
 * Bio-Medicine August, 2008
 * FEEDZILLA August, 2008
 * EurekAlert! August, 2008
 * FirstScience News August, 2008
 * Latest News August, 2008
 * ICONOCAST August, 2008
 * ICONOCAST Spanish August, 2008
 * PHYSORG.com August, 2008
 * Science Codex August, 2008
 * www.scientificblogging.com August, 2008
 * Thaindian News August, 2008
 * polit.ru August, 2008
 * infuture.ru August, 2008
 * The Smart Techie August, 2008
 * Scientific texts in 3D with interactive formats developed Silicon India August, 2008
 * Scientific texts in 3D with interactive formats developed newKerala.com August, 2008
 * 3D interactive text formats developed, NDTV.com August, 2008
 * innovations report August, 2008
 * Medical News Today August, 2008
 * Online wiki hosts interactive, 3D molecular structures, iTnews August, 2008
 * Scientific texts in 3D with interactive formats developed, SiFy news August, 2008

Abstract Re-Posts

 * Your Lab Data August, 2008
 * find-health-articles.com. November, 2008

Miscellaneous Postings

 * Nominated for Best Website in the Labbies Awards by the TheScientist.com June, 2010
 * digg.com/tech_news digg/Tech News August, 2008
 * StumbleUpon August, 2008
 * TIEDE.fi August, 2008

Talks in Meetings and Seminars

 * Proteopedia - a Scientific 'Wiki' Bridging the Rift Between 3D Structure and Function of Biomacromolecules, HUGO's 13th Human Genome Meeting, September, 2008.
 * In I am not a PDBid I am a Biological Macromolecule, the keynote talk at 3DSig 2008, Structural Bioinformatics and Computational Biophysics (an ISMB satellite meeting Toronto, 18-19 July 2008), Philip E. Bourne discussed removing the barrier between the literature and the PDB, featuring his BioLit project. In this context, he listed Proteopedia as Possibility 1, "a completely new beginning", and discussed its advantages (anyone can contribute leading to wiki quality) and disadvantages (reward for authoring? limitations of wiki format).

Training Workshops

 * Short courses and one-day workshops are taught by Eric Martz on macromolecular structure visualization and structural bioinformatics. These now include a segment on Proteopedia, including use of Proteopedia's Scene-Authoring Tools. In 2008, these have been at the Weizmann Institute of Science in Israel, and at Osaka University and the Okinawa Institute of Science and Technology in Japan. For curricula and upcoming dates, please see Workshops.MolviZ.Org. August, 2008.